I have IPsecs between few OpenBSD machines (release: 4.6, 4.8 $ 4.9). IPsec is working fine for a long time, but here and there (at once, or at twice per day), IPsec traffic just stop. This kind of problem last ussually 17-18 minutes. SAs are still there (or, at least, ipsecctl show that), but traffic cant pass from netA to netB.

I use isakmpd, /etc/ipsec.conf and x509 certificates. There is no nat, no rdr.
Until few months ago, everything worked fine on OBSD 4.5 & 4.6 (So, I think, there is no problem in ipsec.conf or x508).

There are few IPSec users here among the small group of OpenBSD admins on this forum. I'm one, and I have no particular insights into this problem. If you don't get any other advice in the next day or two, consider posting to misc@, perhaps continuing that earlier thread.